March 17, 2014

Last night's second of 13 episodes of "Cosmos- A Spacetime Odyssey" hosted by astrophysicist Neil deGrasse Tyson was "The Rivers of Life" covering evolution and natural selection processes that have made life on Earth as we know it today, and also covers mass extinction events such as asteroid impacts with our planet that have drastically altered the course and progress of life.

In last night's episode Neil deGrasse Tyson asks how did life on Earth begin? A giant step toward solving this puzzle was taken in the 1980's with the Nobel Prize–winning discovery by Tom Cech and Sidney Altman that RNA, the sister molecule of DNA, can catalyze certain chemical reactions inside cells, a job previously thought to be the exclusive domain of proteins. Until their discovery, RNA was thought to have just one function: storing the genetic information cells need to build proteins.

This new revelation about RNA's dual role suggested to some scientists, including Harvard's Jack Szostak, that RNA likely existed long before DNA or proteins because it might be able to catalyze its own reproduction. Their discovery made it easier to think about how life began, Szostak says. "They inspired me to try to think of ways to make RNAs in the lab that could catalyze their own replication."

Szostak and his team is working to recreate a hypothetical model of this process in the laboratory. By building simple cell-like structures in a test tube, they are attempting to establish a plausible path that led primitive cells to emerge from simple chemicals. Ultimately, Szostak hopes to answer fundamental questions about evolution's earliest steps.

Building on earlier work by other scientists, Szostak and colleagues began experimenting with a clay mixture common on early Earth called montmorillonite, which was found to catalyze the chemical reactions needed to make RNA.

So, did life originally spring from clay as some creation myths assert? Not necessarily, but it does provide a possible mechanism for explaining how life initially arose from nonliving molecules. Szostak's team at the Howard Hughes Medical Institute and Massachusetts General Hospital showed that the presence of clay aids naturally occurring reactions that result in the formation of fatty sacks called vesicles, similar to what scientists expect the first living cells to have looked like. Further, the clay helps RNA form. The RNA can stick to the clay and move with it into the vesicles. This provides a method for RNA's critical genetic information to move inside a primitive cell.

"It's exciting because we know that a particular clay mineral helps with the assembly of RNA," Szostak said. "There certainly would have been lots of environments on early Earth with clay minerals. It's something that forms relatively easily as rocks weather."

The researchers also found that the clay expedited the process by which fatty acids form vesicles that could serve as cell membranes. When RNA and fatty acids were mixed with the montmorillonite, the clay seemed to help transport the RNA inside the vesicles, forming a cell-like structure. Szostak and his team surmised that a similar process could possibly have led to the creation of the first cell.

The ancestor of all life on Earth today has been dubbed LUCA, short for Last Universal Common Ancestor. The fact that there must have been a LUCA was first made clear in the 1960s when the genetic code was deciphered and found to be universal (at least on Earth).

"It is generally believed that LUCA was a heat-loving or hyperthermophilic organism. A bit like one of those weird organisms living in the hot vents along the continental ridges deep in the oceans today (above 90 degrees Celsius)," said Nicolas Lartillot, a bio-informatics professor at the Université de Montréal. "However, our data suggests that LUCA was actually sensitive to warmer temperatures and lived in a climate below 50 degrees."

The research team compared genetic information from modern organisms to characterize the ancient ancestor of all life on earth. "Our research is much like studying the etymology of modern languages so as to reveal fundamental things about their evolution," says professor Lartillot. "We identified common genetic traits between animals, plant, bacteria, and used them to create a tree of life with branches representing separate species. These all stemmed from the same trunk – LUCA, the genetic makeup that we then further characterized."

The group's findings are an important step towards reconciling conflicting ideas about LUCA. In particular, they are much more compatible with the theory of an early RNA world, where early life on Earth was composed of ribonucleic acid (RNA), rather than deoxyribonucleic acid (DNA).

However, RNA is particularly sensitive to heat and is unlikely to be stable in the hot temperatures of the early Earth. The data of Dr. Lartillot with his collaborators indicate that LUCA found a cooler micro-climate to develop, which helps resolve this paradox and shows that environmental micro domains played a critical role in the development of life on Earth.

"It is only in a subsequent step that LUCA's descendants discovered the more thermostable DNA molecule, which they independently acquired (presumably from viruses), and used to replace the old and fragile RNA vehicle. This invention allowed them to move away from the small cool microclimate, evolved and diversify into a variety of sophisticated organisms that could tolerate heat," adds Dr. Lartillot.

In a recent breakthrough, a extremely small RNA molecule created by a University of Colorado at Boulder team can catalyze a key reaction needed to synthesize proteins, the building blocks of life. The findings could be a substantial step toward understanding "the very origin of Earthly life," according to Michael Yarus. Indeed, the findings may extend to future discoveries of life beyond Earth: "There may be early RNA-related relics of life on Mars and other places in the solar system, and it will be *very* interesting to see whether it looks like us or not."

According to Yarus, author of Life from an RNA World: The Ancestor Within -Luca evolved the code as a result of natural chemical affinities between nucleotides and amino acids. Chemical bonding, he says, means that different amino acids naturally like to sit next to some triplets and not others.

The genetic code is the consequence of chemical affinities between RNA and amino acids.In other words, the genetic code is the inevitable consequence of affinities between the molecular building blocks of RNA and those of the proteins they code for. If Yarus right, it will explain why individual triplets always code for the same amino acids, whether in a virus or a human.

Yarus works with artificial RNA and has shown that these chemical affinities do exist. Mix strands of RNA with amino acids and the amino acids will more or less spontaneously nestle up to their corresponding triplets. "Yarus found that anticodons [a type of triplet found in some RNAs] were particularly good in this regard and bind the 'correct' amino acid with up to a millionfold greater affinity than other amino acids," says Nick Lane of University College London.

Now David Johnson and Lei Wang of the Salk Institute for Biological Sciences in La Jolla, California, have shown for the first time that these natural affinities occur in real organisms.

Johnson and Wang decided to look for evidence in ribosomes - key components of the cellular machinery that assemble proteins from amino acids. Ribosomes are made of a tangle of RNA and amino acid chains, so if there was natural attraction going on, it should be found there, they reasoned.

Sure enough, when the pair looked at where amino acids sat in the ribosome, they found that 11 of 20 standard amino acids were far more likely than not to be positioned next to the "right" triplet according to the genetic code (Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1000704107).

"Not only is there a chemical reason for these affinities between amino acids and their triplets but you can see them in a natural, biological system," says Yarus. What's more, he adds, the ribosome is an evolutionarily ancient structure, supporting the idea that these affinities go way back. All this, he says, backs his theory that relatively simple chemical interactions allowed Luca to evolve the universal genetic code.

While the genetic code is central to life as we know it, there is no reason to think that other self-replicating life forms have to use it. However, since Ida gave rise to the RNA-based Luca, it is logical to assume Ida was also made of RNA or something very similar. But that creates a problem: how did RNA - made from a long chain of nucleotides - assemble itself?

Nucleotides don't tend to form chains without catalysts to help them. In living cells, those catalysts are always proteins, yet the first proteins were made by Luca; they did not exist in the time of Ida. Something is needed that is like RNA but simple enough to replicate itself without a catalyst.

Cellular RNA can have hundreds or thousands of its basic structural units, called nucleotides. Yarus' team focused on a ribozyme -- a form of RNA that can catalyze chemical reactions -- with only five nucleotides.

The finding adds weight to the "RNA World" hypothesis, which proposes that life on Earth evolved from early forms of RNA.

Yarus noted that the RNA World hypothesis was complicated by the fact that RNA molecules are hard to make. "This work shows that RNA enzymes could have been far smaller, and therefore far easier to make under primitive conditions, than anyone has expected."

If very simple RNA molecules such as the product of the Yarus lab could have accelerated chemical reactions in Earth's primordial stew, the chances are much greater that RNA could direct and accelerate biochemical reactions under primitive conditions.

Before the advent of RNA, most biologists believe, there was a simpler world of chemical replicators that could only make more of themselves, given the raw materials of the time, Yarus said.

"If there exists that kind of mini-catalyst, a ‘sister' to the one we describe, the world of the replicators would also jump a long step closer and we could really feel we were closing in on the first things on Earth that could undergo Darwinian evolution," Yarus said.

"In other words, we may have taken a substantial step toward the very origin of Earthly life," he said. "However, keep well in mind that the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined."

Mass Extinction Events

Since the first organisms appeared on Earth approximately 3.8 billion years ago, life on the planet has had some close calls. In the last 500 million years, Earth has undergone five mass extinctions, including the event 66 million years ago that wiped out the dinosaurs. And while most scientists agree that a giant asteroid was responsible for that extinction, there’s much less consensus on what caused an even more devastating extinction, the end-Permian extinction, that occurred 252.2 million years ago, decimating 90 percent of marine and terrestrial species, from snails and small crustaceans to early forms of lizards and amphibians.

“The Great Dying,” as it’s now known, was the most severe mass extinction in Earth’s history, and is probably the closest life has come to being completely extinguished. Possible causes include immense volcanic eruptions, rapid depletion of oxygen in the oceans, and — an unlikely option — an asteroid collision.

While the causes of this global catastrophe are unknown, an MIT-led team of researchers established in that the end-Permian extinction was extremely rapid, triggering massive die-outs both in the oceans and on land in less than 20,000 years — the blink of an eye in geologic time. The MIT team also found that this time period coincides with a massive buildup of atmospheric carbon dioxide, which likely triggered the simultaneous collapse of species in the oceans and on land.

“We’ve got the extinction nailed in absolute time and duration,” says Sam Bowring, the Robert R. Shrock Professor of Earth and Planetary Sciences at MIT. “How do you kill 96 percent of everything that lived in the oceans in tens of thousands of years? It could be that an exceptional extinction requires an exceptional explanation.”

The research team at MIT has determined that the end-Permian extinction occurred over 60,000 years, give or take 48,000 years — practically instantaneous, from a geologic perspective. The new timescale is based on more precise dating techniques, and indicates that the most severe extinction in history may have happened more than 10 times faster than scientists had previously thought.

In addition to establishing the extinction’s duration, Bowring, graduate student Seth Burgess, and a colleague from the Nanjing Institute of Geology and Paleontology also found that, 10,000 years before the die-off, , the oceans experienced a pulse of light carbon, which likely reflects a massive addition of carbon dioxide to the atmosphere. This dramatic change may have led to widespread ocean acidification and increased sea temperatures by 10 degrees Celsius or more, killing the majority of sea life.

But what originally triggered the spike in carbon dioxide? The leading theory among geologists and paleontologists has to do with widespread, long-lasting volcanic eruptions from the Siberian Traps, a region of Russia whose steplike hills are a result of repeated eruptions of magma. To determine whether eruptions from the Siberian Traps triggered a massive increase in oceanic carbon dioxide, Burgess and Bowring are using similar dating techniques to establish a timescale for the Permian period’s volcanic eruptions that are estimated to have covered over five million cubic kilometers.

“It is clear that whatever triggered extinction must have acted very quickly,” says Burgess, the lead author of a paper that reports the results in this week’s Proceedings of the National Academy of Sciences, “fast enough to destabilize the biosphere before the majority of plant and animal life had time to adapt in an effort to survive.”

In 2006, Bowring and his students made a trip to Meishan, China, a region whose rock formations bear evidence of the end-Permian extinction; geochronologists and paleontologists have flocked to the area to look for clues in its layers of sedimentary rock. In particular, scientists have focused on a section of rock that is thought to delineate the end of the Permian, and the beginning of the Triassic, based on evidence such as the number of fossils found in surrounding rock layers.

Bowring sampled rocks from this area (above), as well as from nearby alternating layers of volcanic ash beds and fossil-bearing rocks. After analyzing the rocks in the lab, his team reported in 2011 that the end-Permian likely lasted less than 200,000 years. However, this timeframe still wasn’t precise enough to draw any conclusions about what caused the extinction.

Now, the team has revised its estimates using more accurate dating techniques based on a better understanding of uncertainties in timescale measurements.

With this knowledge, Bowring and his colleagues reanalyzed rock samples collected from five volcanic ash beds at the Permian-Triassic boundary. The researchers pulverized rocks and separated out tiny zircon crystals containing a mix of uranium and lead. They then isolated uranium from lead, and measured the ratios of both isotopes to determine the age of each rock sample.

From their measurements, the researchers determined a much more precise “age model” for the end-Permian extinction, which now appears to have lasted about 60,000 years — with an uncertainty of 48,000 years — and was immediately preceded by a sharp increase in carbon dioxide in the oceans.

The new timeline adds weight to the theory that the extinction was triggered by massive volcanic eruptions from the Siberian Traps that released volatile chemicals, including carbon dioxide, into the atmosphere and oceans. With such a short extinction timeline, Bowring says it is possible that a single, catastrophic pulse of magmatic activity triggered an almost instantaneous collapse of all global ecosystems.

Andrew Knoll, a professor of earth and planetary sciences at Harvard University, says the group’s refined timeline will give scientists an opportunity to test whether the timing of the Siberian Traps eruptions coincides with the extinction.

“Most mechanisms proposed to account for the observed pattern of extinction rely on rapid environmental change, so the sharp constraints on timing also serve as tests of these ideas,” Knoll says. “[This new timeline] bring us closer to the resolution of a major problem posed by the geologic record.”

To confirm whether the Siberian Traps are indeed the extinction’s smoking gun, Burgess and Bowring plan to determine an equally precise timeline for the Siberian Traps eruptions, and will compare it to the new extinction timeline to see where the two events overlap. The researchers will investigate additional areas in China to see if the duration of the extinction can be even more precisely determined.

“We’ve refined our approach, and now we have higher accuracy and precision,” Bowring says. “You can think of it as slowly spiraling in toward the truth.”

The Daily Galaxy via MIT, University of Montreal, yarus@colorado.edu, and hhmi.org

Same old mid-20th Century Neo-Darwinian dogma here. Everything has a physiological mechanism, so says Dr. Tyson as God, preaching the new religion of science from his pulpit on high. Once there was a grizzly bear, and through a mistake in the transcription of DNA, the gene for white fur was selected. And presto! We have the polar bear. It's not as simple as that. This is science dumbed down to the grade-school level, yet booming with portent and authority. I believe evolution is an everyday fact, let's be clear on that. But it's a much more intricate and complicated process than is made out in this series. Self-organization and emergent order are not even mentioned as players. And the transition from the micro-world of genetic "variation and mutation" to the macro-world where they are expressed in complex physiological and behavioral traits, is not just inadequately explained, it's not even looked at. Even consciousness, as asserted by Dr. Tyson and his cohorts, is considered to be nothing more than a by-product of neural activity in the brain. As for life itself, well, they must be confident it will be found somewhere on the electromagnetic spectrum. I found the show really boring and somehow regressive. Old school ideas that are badly in need of an adaptation of their own to 21st Century ideas and thinking. Still the old mechanistic, empirical, reductionist dinosaurs at work here.

Pulswaithe: "Still the old mechanistic, empirical, reductionist dinosaurs at work here."

Are you kidding? The show is a presentation for the general public, which, as shown by the fact that Oklahoma blacked-out the segments on evolution, and by the comments all over the internet, has difficulty understanding and coming to terms with 17th century Newtonian physics and has never accepted 19th century Darwinian biology. "21st Century ideas and thinking"???? Bwwwwaaaahahahahahaha.

You want 21st century thinking? Here's 21st century thinking, as fresh as today's smog in Beijing:

BAN AND BURN. Science is all a big liberal lie. There's no such thing as atoms or molecules. That's all a lie. There's no wavelengths. Radios and TV's and cell just work that way. There's no rockets and anything like that. There' s no atom bomb, ever. That was just a lot of TNT. Computers just work that way, cause God made them like that. Not science. All science books should be banned and burned. BAN AN BURN.

Mr. De-Grasse Tyson needs to learn how to talk to adults. A tiny spaceship (?! really ?) going through the body of the bear takes waaaaaayyy too long, and then he cuts in with "Almost there". At that point I almost considered turning the show off. It's ok to talk to us, but why talk down to us ? Even a reasonably intelligent person can see how very simplistic they are trying to make this show.

I wanted to like this series, but the production/pacing of the story line is awful. It feels like different sections of each hour was edited by different producers and strung together at the last minute. Staging Mr. Neil Degrasse Tyson peering into empty rooms of a virtual museum with no dialogue make awkward television and then delivering important scientific information quickly at the end of a segment is confusing. This show deserves a better producer who understands pacing and continuity. I feel embarrassed for Mr. Tyson.

Everyone has the right to their own opinion. It is when we force our opinions upon others that we are the narrow-minded. This series is just an opinion based on what they believe. It is neither the truth nor a lie. As man matures he discovers many things that change his way of thinking, both in creationism and evolutionary. It is when we can accept the other man’s right to his opinion, can we grow. Only then can we come to an understanding how close the two concepts really mesh. One cannot exist without the other. You cannot teach calculus to someone who does not understand algebra.

@Dennis some opinions are stupid. Some opinions are worthless. Some opinions are dangerous. Some opinions have no evidence to support their veracity. Some opinions are wrong. Some opinions should remain silent. I am not convinced that everyone is entitled to their opinion...

@ adam you're completely missing the point I was trying to make. You're talking about the world that is still stuck in the Middle Ages. I'm talking about the world that has moved on from where Dr. Tyson is.